Thanks for the confirmation. I'm looking for contacts among solvent
molecule, so there's no concept of a "native structure" in this case. I'll
find the contacts some other way, then.
On Mon, Aug 3, 2015 at 9:07 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Sun, 2015-08-02 at 18:47 -0400, Jose Borreguero wrote:
> > Dear AMBER users,
> >
> > >From the results I'm getting it would seem that the "contacts" command
> of
> > cpptraj does not implement imaging. Can anyone please confirm this?
> >
> > My input script evaluating contact between atom "C" of residues 4124 and
> > 1150:
> >
> > trajin equil.dcd 5001 5001
> > 1
> >
> > distance :4124.C :1150.C out
> > junk.dat
> >
> > contacts (:4124,1150)&.C distance 7.0 out
> > junk2.dat
> > go
> >
> > quit
> >
> > I execute as: cpptraj -p pdbfile -i inputScriptFile
> >
> > The contents of junk.dat:
> > #Frame Dis_00000
> > 1 6.0495
> >
> > The contents of junk2.dat:
> > #time Contacts native Contacts
> > 1.00 0 0
> >
> > There's a discrepance here, since the distance of 6.0495 is well below my
> > 7. 0 cutoff. I should be getting one contact
>
> As your observations here note, the "contacts" action does not account
> for imaging (you can verify this in the source code). However, the
> "nativecontacts" command, which probably does what you want it do,
> *does* account for imaging (unless you explicitly request that it not
> via the `noimage` keyword).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Mon Aug 03 2015 - 10:00:02 PDT
